Date post: | 06-Jan-2017 |
Category: |
Science |
Upload: | nathan-dunn |
View: | 185 times |
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NathanADunn1,MonicaC.Munoz-Torres1,ColinDiesh2,DeepakUnni2,EricYao3,IanHolmes3,
ChristineG.Elsik2andSuzannaLewis1
(1)LawrenceBerkeleyNationalLaboratory,Berkeley,CA,(2)DivisionofAnimalSciences,UniversityofMissouri,Columbia,MO,(3)DepartmentofBioengineering,Berkeley,CA
Apollo:ImprovingCollaborativeGenomeAnnotation
h t t p s : / /g i t h ub . o r g /GMOD/Apo l l o /
h t t p : / /genomea r c h i t e c t . o r g /
GenomeAnnotationStructuralAnnotation• exons,introns,UTRs• repeatregions• transpelements
• molecularevolution• sequenceconservation
FunctionalAnnotation• GeneOntology
• molecularfunction• biologicalprocess• cellularcomponent
• expression• metabolicpathways/functions• genefamilies
Experimental design, sampling
Comparative analyses
Consensus Gene Set
Manual Annotation
Automated Annotation
Sequencing Create Assembly
Synthesis & dissemination
ExampleGenomeAnalysisWorkflowManytools•Manypeople•Lotsofdata•ManyIterations
AnnotationFGENESH
AutomatedIdentificationofGenomicFeatures
Automated Annotation
GenerationofGeneModelsfindORFs,multipleroundsofgeneprediction,etc.AnnotationofGeneModelsDescribingfunction,expressionpatterns,metabolicnetworkmemberships
• Assemblyerrorscancausefragmentedannotations
• Limitedcoveragemakespreciseidentificationdifficult
Manual Annotation
Human Analysis
Automated Annotation
ManualAnnotationRefinesFeatures
Experimental Evidence
cDNAs,HMMdomainsearches,RNAseq,genesfromotherspecies.
• Additionaldata• Biologicalknowledge• Curatorexperience
Manual Annotation
AnnotatorsApollo
Google Web Toolkit (GWT) / Bootstrap
WhatisApollo?Annotators
ApolloGoogle Web Toolkit (GWT) / Bootstrap
Annotators
ApolloGoogle Web Toolkit (GWT) / Bootstrap
• Web-basedGenomeEditor• JBrowse• Real-timecollaborative• AutomaticSave
Photo Credits: i5K; Alex Wild at http://www.alexanderwild.com/: leaf cutter ant, ensign wasp; Leo Bukeboom: Nasonia vitripennis jewel wasp; Wikimedia Commons: Apis mellifera honey bee; Mike MacNeil USDA/ARS Fort Keogh LARRL: Bos taurus cow.
ApolloGenomeEditorNavigation
UserAnnotations
Evidence
Transcripts(GFF3,GBK)
BAMReads
Transcripts(GFF3,GBK)
BigWigXY
BigWigHeatMap
CreateAnnotationbyDragging/Right-click
CustomColorSchemes
ColorCDSFrame
HowtoEditData?SequenceAlterations
EditStructurebyDraggingorPopupMenu
History,Undo/Redo
EditFunctionalData
• PubMed/xdbref
• GeneOntology
• Metadata
• key/value
• status
• comments
NavigatewhileViewingGenome
• Allowsusersanalternatedimensionstonavigateandedit• Well-establishedparadigmfor“editing”inapplications
Resizable/Closeable ShareableLinks
SearchAnnotationsandDiscoverDetails
Search
Navigation
View/EditDetails
ExploreandExportSequences
Search
Navigation
AddandShareOrganisms
AddorganismsfromexistingJBrowsedirectory
Specify“Public”organismsthatdonotrequirealogin
ManageWhoSeesWhat
Add/SearchUsers
EditUserOrganismPermission
UserCan“Admin”anOrganism
WorkwithLotsofUsersandOrganisms
AddUsertoGroupswithPermissions
SetBulkUserPermissionsusingGroups
HowtogetApollointoyourWorkFlow?
Reports
DataInput
DataOutput
Analysis
Authentication
BLAT(built-in)
RemoteBLAST
ExampleWorkflow
ServerCriteria
ApolloServer
FileSystem
JBrowseDirectories
Security
• Quicksetupandeasytodeploy
• Plugins(websockets,security,etc.)• Scaleable• RapidApplicationDevelopment
• Integratedtesting• Bonus:Minimalchanges• Matureandwell-supported DataStore
• Thread-safetransactions
• Transparent/Queryable• Structured• SimpleSetup
RESTWebSocket
Considerations• Node.js• RubyonRails
• Grails• Struts,SpringMVC,etc.• Django,Php,etc.
JBrowse
Clients
GrailsServer
ApolloServer-Grails
JDBC
FileSystem
JBrowseDirectories
Security
• QuickSetup• Plugins• Scaleable(Spring/Hibernate/JVM)• RapidApplicationDevelopment• Integratedtesting• ExistingJBrowsetracks
DataStore• Thread-safetransactions• POJO(NoXML)• MultipleDBsupport• Structured
RESTWebSocket
JBrowse
Clients
• IntegratewithJBrowse• UsesexposedREST• Buildyourowninterface
• BuildComplexUI• Well-supported• IsJavaScriptatsomelevel
SidebarClientCriteria
OftheMillionAvailableOptions• Angular+Bootstrap• jQueryalltheway• GWT+Bootstrap• Dojo• OtherIdeas:React,Polymer,etc.
Annotators
ApolloGoogle Web Toolkit (GWT) / BootstrapJBrowse
DOJO / jQuery
ApolloJBrowse
RESTWebSocket
GWT• Java->JSOptimizedCross-Compiler• GoogleusesforComplexUI(Gmail,
Sheets,Adwords)• UsesexposedREST• Buildyourowninterface(morehere)• CanstilluseJS/HTMLwherever
GWTSidebarClient
JBrowseGenomicViewer• Websocketsimproved
reliability/performance
Annotators
ApolloGoogle Web Toolkit (GWT) / BootstrapJBrowse
DOJO / jQueryApolloJBrowse
RESTWebSocket
ScriptableWebServices• Examples:Groovy,Perl,shell• AutogeneratedAPI-docinApollo
curl -d "{ 'operation': 'get_features', ‘track':'Group1.10','username':'[email protected]','password':'demo'}" http://localhost:8080/apollo/AnnotationEditorService
ApolloServer-Grails
Security
JBrowseDirectories
Architecture
WebServicesClient
Perl,Shell,Groovy,PHP,etc.
Annotators
ApolloGoogle Web Toolkit (GWT) / BootstrapJBrowse
DOJO / jQuery
REST RESTWebSocket
JDBC
FileSystem
ApolloJBrowse
• apollo-config.groovy
• Webservices
• Grailsplugin
• JBrowseplugin
• Database
• Fork
• Ask
• Hackathon(Jan14,Scripps)
HowtomakechangesandconnecttoApollo
h t t p s : / /g i t h ub . o r g /GMOD/Apo l l o /
apo l l o@ l i s t s . l b l . g o v
ExampleIntegrations
GalaxyDocker
GFF3output,scriptsWebservices
VectorBase
iPlantCollaborative
ManualAnnotationwithApolloImprovesGeneModels
Improveannotations•Multipleevidencesources•Remotecollaborators•Workonmultipleorganisms•Publishimprovedgenesets
Enablecuratorstodotheirjob• Managemultipleorganisms• Manageusersandgroups• Integratecurationpipeline• ExtendApollotomeetneeds
Reports
ImportEvidence(JBrowse) Export
CuratedGenome
Analysis
Curate
Edit
GFF3
BAM
BigWig
Explore
Group20 Group31
FutureWork
Mavenize
WebApollo
DesktopApollo
DBbackend,Sidebar,Grails,Multi-organism,WS
1.0
2.0
Projection2.1
2.2 Variant/phenotypeannotation
2.3HumanData/Client-sideOptimization
Collapseintronsandspacebetweenfeatures
Bringscaffoldstogether
Viewandlinkgenesacrossscaffolds
• BerkeleyBioinformaticsOpen-sourceProjects(BBOP),BerkeleyLab:ApolloandGeneOntologyteams.SuzannaE.Lewis(PI).
• §ChristineG.Elsik(PI).UniversityofMissouri.
• *IanHolmes(PI).UniversityofCaliforniaBerkeley.
• StephenFicklin,GenSAS,WashingtonStateUniversity
• ApolloissupportedbyNIHgrants5R01GM080203fromNIGMS,and5R01HG004483fromNHGRI.AlsosupportedbytheDirector,OfficeofScience,OfficeofBasicEnergySciences,oftheU.S.DepartmentofEnergyunderContractNo.DE-AC02-05CH11231
• AlexWildathttp://www.alexanderwild.com/:leafcutterant,ensignwasp;LeoBukeboom:Nasoniavitripennisjewelwasp;WikimediaCommons:Apismelliferahoneybee;MikeMacNeilUSDA/ARS
• ThankstoyouandtheApollo/GMODCommunities
Apollo
MonicaMunoz-Torres
NathanDunn
ColinDiesh§
DeepakUnni§
JBrowse
EricYao
*GeneOntology
ChrisMungall
SethCarbon
HeikoDietze
BBOP
Apollo:http://GenomeArchitect.org
https://github.org/GMOD/Apollo/
Questions?
NALatUSDA
ChristopherChilders
MonicaPoelchau
Mei-JuChen
Yu-Yu“Fish”Lin
GaryMoore
United States Department of AgricultureNational Institute of Food and Agriculture